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scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution.
Zhu, Sheng; Lian, Qiwei; Ye, Wenbin; Qin, Wei; Wu, Zhe; Ji, Guoli; Wu, Xiaohui.
Afiliación
  • Zhu S; Pasteurien College, Soochow University, Suzhou, Jiangsu 215000, China.
  • Lian Q; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
  • Ye W; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
  • Qin W; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
  • Wu Z; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
  • Ji G; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
  • Wu X; Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.
Nucleic Acids Res ; 50(D1): D365-D370, 2022 01 07.
Article en En | MEDLINE | ID: mdl-34508354
ABSTRACT
Alternative polyadenylation (APA) is a widespread regulatory mechanism of transcript diversification in eukaryotes, which is increasingly recognized as an important layer for eukaryotic gene expression. Recent studies based on single-cell RNA-seq (scRNA-seq) have revealed cell-to-cell heterogeneity in APA usage and APA dynamics across different cell types in various tissues, biological processes and diseases. However, currently available APA databases were all collected from bulk 3'-seq and/or RNA-seq data, and no existing database has provided APA information at single-cell resolution. Here, we present a user-friendly database called scAPAdb (http//www.bmibig.cn/scAPAdb), which provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level. Currently, scAPAdb collects APA information from > 360 scRNA-seq experiments, covering six species including human, mouse and several other plant species. scAPAdb also provides batch download of data, and users can query the database through a variety of keywords such as gene identifier, gene function and accession number. scAPAdb would be a valuable and extendable resource for the study of cell-to-cell heterogeneity in APA isoform usages and APA-mediated gene regulation at the single-cell level under diverse cell types, tissues and species.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Interfaz Usuario-Computador / ARN Mensajero / Proteínas de Unión al ARN / Regiones no Traducidas 3' / Poliadenilación / Bases de Datos Genéticas Límite: Animals / Humans Idioma: En Revista: Nucleic Acids Res Año: 2022 Tipo del documento: Article País de afiliación: China

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Interfaz Usuario-Computador / ARN Mensajero / Proteínas de Unión al ARN / Regiones no Traducidas 3' / Poliadenilación / Bases de Datos Genéticas Límite: Animals / Humans Idioma: En Revista: Nucleic Acids Res Año: 2022 Tipo del documento: Article País de afiliación: China